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One more way to parse the sequence. The initialization statement is only needed if zero-counts must be defined.

use strict; use warnings; use Readonly; use Data::Dumper qw( Dumper ); Readonly::Scalar my $seq => "ATCGGCGCCTAT" ; my %count; @count{ qw(A1 A2 A3 T1 T2 T3 C1 C2 C3 G1 G2 G3 ) } = (0) x (3*4); foreach my $i (0 .. length($seq)-1 ) { my $pos = $i % 3 + 1; my $base = substr $seq, $i, 1; $count{$base.$pos}++; } $Data::Dumper::Sortkeys = 1; print Dumper \%count;

Or if you really want individual scalar counts and do not mind global variables or symbolic references.

use strict; use warnings; my $seq = 'ATCGGCGCCTAT' ; my %count; our( $A1, $A2, $A3, $T1, $T2, $T3, $C1, $C2, $C3, $G1, $G2, $G3 ) = (0) x 12; foreach my $i (0 .. length($seq)-1 ) { my $pos = $i % 3 + 1; my $base = substr $seq, $i, 1; {no strict 'refs'; ${$base.$pos}++;} } print $A1, $A2, $A3, $T1, $T2, $T3, $C1, $C2, $C3, $G1, $G2, $G3;

In reply to Re: How can I count the number and kinds of letters at 1st, 2nd and 3rd positions of 3-letter words in a string? by BillKSmith
in thread How can I count the number and kinds of letters at 1st, 2nd and 3rd positions of 3-letter words in a string? by supriyoch_2008

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